X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSearchResults.java;h=909a0fef644be43cff883bbf3eb047bb670285eb;hb=ff8a85b4462d824e858b9ce57082455772e1a2ff;hp=e87b5f022ce457338bc1c98bbd1b55a358b8b211;hpb=745806901cdcda04d9b5c496cb5249a03af19971;p=jalview.git

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index e87b5f0..909a0fe 100755
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -33,6 +33,7 @@ import java.util.List;
  */
 public class SearchResults implements SearchResultsI
 {
+  private int count;
 
   private List<SearchResultMatchI> matches = new ArrayList<>();
 
@@ -168,18 +169,41 @@ public class SearchResults implements SearchResultsI
     if (!matches.contains(m))
     {
       matches.add(m);
+      count++;
     }
     return m;
   }
 
   @Override
+  public void addResult(SequenceI seq, int[] positions)
+  {
+    /*
+     * we only increment the match count by 1 - or not at all,
+     * if the matches are all duplicates of existing
+     */
+    int beforeCount = count;
+    for (int i = 0; i < positions.length - 1; i += 2)
+    {
+      addResult(seq, positions[i], positions[i + 1]);
+    }
+    if (count > beforeCount)
+    {
+      count = beforeCount + 1;
+    }
+  }
+
+  @Override
   public boolean involvesSequence(SequenceI sequence)
   {
+    final int start = sequence.getStart();
+    final int end = sequence.getEnd();
+
     SequenceI ds = sequence.getDatasetSequence();
-    for (SearchResultMatchI _m : matches)
+    for (SearchResultMatchI m : matches)
     {
-      SequenceI matched = _m.getSequence();
-      if (matched != null && (matched == sequence || matched == ds))
+      SequenceI matched = m.getSequence();
+      if (matched != null && (matched == sequence || matched == ds)
+              && (m.getEnd() >= start) && (m.getStart() <= end))
       {
         return true;
       }
@@ -210,8 +234,8 @@ public class SearchResults implements SearchResultsI
       {
         mfound = true;
         matchStart = sequence.findIndex(m.start) - 1;
-        matchEnd = m.start == m.end ? matchStart : sequence
-                .findIndex(m.end) - 1;
+        matchEnd = m.start == m.end ? matchStart
+                : sequence.findIndex(m.end) - 1;
       }
 
       if (mfound)
@@ -258,9 +282,12 @@ public class SearchResults implements SearchResultsI
   {
     int count = 0;
     BitSet mask = new BitSet();
+    int startRes = sqcol.getStartRes();
+    int endRes = sqcol.getEndRes();
+
     for (SequenceI s : sqcol.getSequences())
     {
-      int[] cols = getResults(s, sqcol.getStartRes(), sqcol.getEndRes());
+      int[] cols = getResults(s, startRes, endRes);
       if (cols != null)
       {
         for (int pair = 0; pair < cols.length; pair += 2)
@@ -279,9 +306,9 @@ public class SearchResults implements SearchResultsI
   }
 
   @Override
-  public int getSize()
+  public int getCount()
   {
-    return matches.size();
+    return count;
   }
 
   @Override
@@ -322,8 +349,10 @@ public class SearchResults implements SearchResultsI
   }
 
   /**
-   * Two SearchResults are considered equal if they contain the same matches in
-   * the same order.
+   * Two SearchResults are considered equal if they contain the same matches
+   * (Sequence, start position, end position) in the same order
+   * 
+   * @see Match#equals(Object)
    */
   @Override
   public boolean equals(Object obj)
@@ -341,4 +370,27 @@ public class SearchResults implements SearchResultsI
   {
     matches.addAll(toAdd.getResults());
   }
+
+  @Override
+  public List<SequenceI> getMatchingSubSequences()
+  {
+    List<SequenceI> seqs = new ArrayList<>();
+
+    /*
+     * assemble dataset sequences, and template new sequence features,
+     * for the amend features dialog
+     */
+    for (SearchResultMatchI match : matches)
+    {
+      SequenceI seq = match.getSequence();
+      while (seq.getDatasetSequence() != null)
+      {
+        seq = seq.getDatasetSequence();
+      }
+      // getSubSequence is index-base0, findIndex returns index-base1
+      seqs.add(seq.getSubSequence(seq.findIndex(match.getStart()) - 1,
+              seq.findIndex(match.getEnd())));
+    }
+    return seqs;
+  }
 }